Integrated Microbiome
Analysis Pipelines

Fostering continuous improvement and integration

Quick Glimpse

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We use snakemake [@Dadasnake2021] to maintain reproducibility and improvement of the bioinformatics analysis of microbiome data.

Microbial Profiling Options

Classification of Operational Taxonomic Units (OTUs)

• OTUs are clusters with sequence similarity and are accepted as an analytical unit used in microbial profiling using 16S rRNA gene markers.

Classification of Phylotype

• A phylotype in microbiome research is a DNA sequence or group of sequences sharing more than an arbitrarily chosen level of similarity of a 16S rRNA gene marker.

Classification of Amplicon Sequence Variant (ASV)

• An ASV in microbiome research is any one of the inferred single DNA sequences recovered from a bioinformatics analysis of 16S rRNA marker genes.

Classification of Microbiaal Phylogenies

• Microbial phylogenies are estimated from gene sequences homologies and using models of mutation to infer most-likely evolutionary histories.

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Mothur Microbiome Snakemake Workflow

Reference links

• https://github.com/wclose/mothurPipeline

Example of common FAQs (in progress)

1. Mothur dist.seqs taking too long.
• Length of the merged reads (merged reads over 300pb).
• Not enough overlaping when merging the paired reads.
• Use other pre-cluster algorithm like Deblur.
• Too many uniques?
• Not enough computer power?: Use HPC or Cluster.
• Try to make contigs using maxee instead of deltaq or use phylogeny approach for downstream analysis, or use clister.split based on taxonomy.
• do not forget to use controls.

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Last updated on January 20, 2023.

These workflows are continuously reviewed, integrated, tested and compiled by Teresia Mrema-Buza.
Github_Repo: https://github.com/tmbuza/imap-mothur.
Github_Page (this document): https://tmbuza.github.io/imap-mothur/.
Visit the Complex Data Insights (CDI) website for more practical user guides (…in progress).

References